Question: AnnotatedDataFrame metadata bug?
5.4 years ago by
Adrienne Stilp • 30
Adrienne Stilp • 30 wrote:
Hi Bioconductors, I recently noticed some unexpected behavior for AnnotatedDataFrame metadata. If you have an annotated data frame with metadata and add a new variable whose name is a shortened version of an existing variable, the metadata for the newly-added variable is set to the metadata of the existing variable. Here's an example: library(Biobase) annot <- AnnotatedDataFrame(data.frame(myvariable=runif(10))) varMetadata(annot)["myvariable", "labelDescription"] <- "random samples from a uniform distribution" annot$myvar <- rnorm(10) annot$newvar <- rnorm(10) annot[["myvari"]] <- rnorm(10) varMetadata(annot) For me, this last step prints out: labelDescription myvariable random samples from a uniform distribution myvar random samples from a uniform distribution newvar <na> myvari random samples from a uniform distribution even though I've only set the metadata for myvariable. I would expect that any new variables have NA for metadata, which is true for "newvar" above, but is not the case for the variables whose names are a shortened version of "myvariable" ("myvar" and "myvari"). I end up with misleading or incorrect metadata for the new variables "myvar" and "myvari". The can always be changed later, but I often see what metadata I need to update at the end by checking which have NA labelDescriptions, so these new variables wouldn't show up. I'm using bioc-devel. Here's the sessionInfo() output: R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached):  tools_3.0.2 Thanks, Adrienne
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